TSR1

TSR1 ribosome maturation factor, the group of Ribosomal biogenesis factors|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 17:2322396-2336657

Links

ENSG00000167721 ∙ NCBI:55720 ∙ OMIM:611214 ∙ HGNC:25542 ∙ Uniprot:Q2NL82 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			49	3	2	54
nonsense						0
start loss						0
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			8			8
Total	0	0	58	4	3

Variants in TSR1

This is a list of pathogenic ClinVar variants found in the TSR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-2323161-A-G		not specified	Uncertain significance (Oct 27, 2023)
17-2323211-G-A		not specified	Uncertain significance (Jan 18, 2023)
17-2323275-G-A		not specified	Uncertain significance (Jan 19, 2022)
17-2323314-A-G		not specified	Uncertain significance (Jun 24, 2022)
17-2323317-T-A		not specified	Uncertain significance (May 08, 2024)
17-2323736-C-G		not specified	Uncertain significance (Dec 15, 2022)
17-2323738-A-C		not specified	Uncertain significance (Aug 04, 2023)
17-2323751-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-2323860-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-2324231-T-C		not specified	Uncertain significance (Dec 19, 2023)
17-2324249-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-2324254-G-C		not specified	Uncertain significance (Nov 22, 2021)
17-2324278-G-A		TSR1-related disorder	Likely benign (Sep 21, 2020)
17-2324302-T-C		not specified	Uncertain significance (Jun 02, 2023)
17-2324335-A-C		not specified	Uncertain significance (Jun 18, 2021)
17-2324337-C-A		not specified	Uncertain significance (Jul 26, 2022)
17-2324510-G-T		not specified	Uncertain significance (Apr 14, 2022)
17-2324542-G-A		not specified	Uncertain significance (Feb 21, 2024)
17-2324707-A-C		not specified	Uncertain significance (May 18, 2023)
17-2324733-A-G		not specified	Uncertain significance (Jul 09, 2021)
17-2324814-A-G		not specified	Uncertain significance (Mar 01, 2024)
17-2325306-T-C		not specified	Uncertain significance (Mar 31, 2024)
17-2325369-G-A		not specified	Likely benign (May 11, 2022)
17-2325413-T-A		not specified	Uncertain significance (Jun 21, 2023)
17-2325420-G-A		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSR1	protein_coding	protein_coding	ENST00000301364	15	15005

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.16e-21	0.0201	125585	0	163	125748	0.000648

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0643	445	441	1.01	0.0000224	5299
Missense in Polyphen		144	149.63	0.96235		1754
Synonymous	-0.334	166	161	1.03	0.00000803	1519
Loss of Function	0.924	35	41.4	0.845	0.00000229	470

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00145
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00120	0.00103
Finnish	0.000747	0.000739
European (Non-Finnish)	0.000463	0.000457
Middle Eastern	0.00120	0.00103
South Asian	0.000737	0.000719
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required during maturation of the 40S ribosomal subunit in the nucleolus. {ECO:0000250}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.985
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.1

Haploinsufficiency Scores

• pHI: 0.843
• hipred: N
• hipred_score: 0.498
• ghis: 0.615

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tsr1

Gene ontology

• Biological process: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• Cellular component: nucleoplasm;nucleolus;cytosol;preribosome, small subunit precursor
• Molecular function: RNA binding;GTPase activity;GTP binding;U3 snoRNA binding